WikiPathways: connecting communities.

Nucleic Acids Research
Marvin MartensMartina Kutmon

Abstract

WikiPathways (https://www.wikipathways.org) is a biological pathway database known for its collaborative nature and open science approaches. With the core idea of the scientific community developing and curating biological knowledge in pathway models, WikiPathways lowers all barriers for accessing and using its content. Increasingly more content creators, initiatives, projects and tools have started using WikiPathways. Central in this growth and increased use of WikiPathways are the various communities that focus on particular subsets of molecular pathways such as for rare diseases and lipid metabolism. Knowledge from published pathway figures helps prioritize pathway development, using optical character and named entity recognition. We show the growth of WikiPathways over the last three years, highlight the new communities and collaborations of pathway authors and curators, and describe various technologies to connect to external resources and initiatives. The road toward a sustainable, community-driven pathway database goes through integration with other resources such as Wikidata and allowing more use, curation and redistribution of WikiPathways content.

References

May 24, 2005·Biochemical and Biophysical Research Communications·Jian WangGuoqing Cao
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Jul 25, 2008·PLoS Biology·Alexander R PicoChris Evelo
Jan 14, 2010·Genome Biology·Kumaran KandasamyAkhilesh Pandey
Sep 8, 2010·Environmental Toxicology and Chemistry·Gerald T AnkleyDaniel L Villeneuve
Nov 19, 2011·Nucleic Acids Research·Thomas KelderAlexander R Pico
Mar 30, 2012·Omics : a Journal of Integrative Biology·Guangchuang YuQing-Yu He
Feb 24, 2015·PLoS Computational Biology·Martina KutmonChris T Evelo
Oct 21, 2015·Nucleic Acids Research·Martina KutmonAlexander R Pico
Mar 16, 2016·Scientific Data·Mark D WilkinsonBarend Mons
May 5, 2016·Nucleic Acids Research·Maxim V KuleshovAvi Ma'ayan
May 21, 2016·PLoS Computational Biology·Anwesha BohlerChris T Evelo
Jun 24, 2016·PLoS Computational Biology·Andra WaagmeesterAlexander R Pico
Feb 6, 2017·Methods in Molecular Biology·Rudolf T PillichDexter Pratt
Jul 21, 2017·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Jessica J Y LeeNenad Blau
Oct 20, 2017·Bioinformatics·Charles Tapley HoytJonathan Wren
Nov 15, 2017·Nucleic Acids Research·Denise N SlenterEgon L Willighagen
Nov 22, 2017·Nucleic Acids Research·Maria LevchenkoJohanna McEntyre
Oct 26, 2018·Nucleic Acids Research·Birgit H M MeldalSandra Orchard
Nov 10, 2018·Clinical and Translational Science·UNKNOWN Biomedical Data Translator Consortium
Dec 20, 2018·NPJ Systems Biology and Applications·Daniel Domingo-FernándezMartin Hofmann-Apitius
Jan 10, 2019·Science Signaling·Valerie B O'DonnellShankar Subramaniam
May 17, 2019·BMC Bioinformatics·Daniel Domingo-FernándezMartin Hofmann-Apitius
May 23, 2019·Nucleic Acids Research·Yuxing LiaoBing Zhang
Jul 13, 2019·Briefings in Bioinformatics·Mitra EbrahimpoorJelle Goeman
Sep 19, 2019·European Journal of Human Genetics : EJHG·Stéphanie Nguengang WakapAna Rath
Dec 12, 2019·Frontiers in Genetics·Sarah MubeenDaniel Domingo-Fernández
Mar 18, 2020·ELife·Andra WaagmeesterAndrew I Su

❮ Previous
Next ❯

Citations

Jan 6, 2021·Nucleic Acids Research·Daniel J Rigden, Xosé M Fernández
Feb 10, 2021·European Journal of Human Genetics : EJHG·Matthew AguirreManuel A Rivas
Feb 27, 2021·Frontiers in Pharmacology·Patric SchymanAnders Wallqvist
Mar 8, 2021·Nucleic Acids Research·Birgit H M MeldalPablo Porras
Apr 14, 2021·Nature Metabolism·Anthony R AngueiraPatrick Seale
Apr 17, 2021·Expert Review of Proteomics·Daniela BraconiAnnalisa Santucci
May 22, 2021·Nature Nanotechnology·Nina JeliazkovaPenny Nymark
May 22, 2021·Nucleic Acids Research·Xuanjin ChengStefan Taubert
Jun 7, 2021·Metabolomics : Official Journal of the Metabolomic Society·Jennifer E KyleBobbie-Jo M Webb-Robertson
Jun 3, 2021·Methods and Protocols·Daniele MercatelliFederico Manuel Giorgi
May 25, 2021·The FEBS Journal·Stephen D GinsbergGabriela Chiosis
Jul 4, 2021·Computers in Biology and Medicine·Daniel Pérez-RodríguezRoberto C Agís-Balboa
Jul 27, 2021·Journal of Neuromuscular Diseases·Stephen MorganWilliam Duddy
Aug 3, 2021·Journal of Cell Communication and Signaling·Shobha DagamajaluT S Keshava Prasad
Aug 13, 2021·IScience·Vasileios L ZogopoulosIoannis Michalopoulos
Aug 28, 2021·Biomolecules·Fotis A BaltoumasGeorgios A Pavlopoulos
Sep 28, 2021·Molecular Systems Biology·Hasmik KeshishianSteven A Carr
Sep 28, 2021·NAR Genomics and Bioinformatics·Sarah MubeenDaniel Domingo-Fernández
Oct 5, 2021·Frontiers in Molecular Biosciences·Nico GerstnerHans-Peter Lenhof
Oct 13, 2021·Bioinformatics·Mukta G PalshikarJuilee Thakar
Nov 9, 2021·Frontiers in Cell and Developmental Biology·Amandine CharrasChristian M Hedrich

❮ Previous
Next ❯

Methods Mentioned

BETA
Profiler

Software Mentioned

WikiPathways REST API
PathMe
WikiPathways SNORQL
ComPath
WikiPathways SPARQL
Smart API
ORPHANET
Ensembl
IUPHAR Guide to
CellDesigner

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.